It should compile your file (if needed), copy it to the Beagle and start gdb on it. However I haven't been able to make it work.

Fix: The first time you try to select the Remote Absolute File Path for C/C++ Application you haven't uploaded the binary file to the Beagle. Hence you cannot select it via the dialogue. Once you clicked the "Debug" button you can re-open the dialogue and select the binary or you can manually complete the line to "/home/MyUsername/workspace/HelloWorld/Debug/HelloWorld".

Back when I had this working, it will run up to main() and wait for your input. Try the single step button (F6 step over, F5 step into)

Other

You might be able to do this via apt-get install. I used the add/remove program app in Red Hat and selected Fedora Eclipse. It appears to load lots of things.
This load version 3.4.1

In Ubuntu go to Applications: Add/Remove
Select Show: All available applications
Search: eclipse
Check: Eclipse
Click: Apply Changes
Wait for some 113 files to download (15 minutes on a fast connection)
With this install you need to load a few more things. Go to
Help:Software Updates:Find and Install...
Select: Search for new features to install
Select: Callisto Discovery Site
Click: Finish (wait a moment)
Select a site near you (wait a moment)
Expand: Callisto Discovery Site
Select: C and C++ Development
Next, Accept, Next, Finish (wait)

I did see the Canymede Update Site on Fedora, so I
Select: Help:Software Updates
Tab: Available Software
Click: Add Site
Location: http://download.eclipse.org/releases/ganymede
Click: OK
The Available Software list should update nad "Ganymede Update Site" should appear. The follow the instructions above.